6TYY

Hedgehog autoprocessing mutant D46H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

General Base Swap Preserves Activity and Expands Substrate Tolerance in Hedgehog Autoprocessing.

Zhao, J.Ciulla, D.A.Xie, J.Wagner, A.G.Castillo, D.A.Zwarycz, A.S.Lin, Z.Beadle, S.Giner, J.L.Li, Z.Li, H.Banavali, N.Callahan, B.P.Wang, C.

(2019) J Am Chem Soc 141: 18380-18384

  • DOI: 10.1021/jacs.9b08914
  • Primary Citation of Related Structures:  
    6TYY

  • PubMed Abstract: 
  • Hedgehog (Hh) autoprocessing converts Hh precursor protein to cholesterylated Hh ligand for downstream signaling. A conserved active-site aspartate residue, D46, plays a key catalytic role in Hh autoprocessing by serving as a general base to activate sub ...

    Hedgehog (Hh) autoprocessing converts Hh precursor protein to cholesterylated Hh ligand for downstream signaling. A conserved active-site aspartate residue, D46, plays a key catalytic role in Hh autoprocessing by serving as a general base to activate substrate cholesterol. Here we report that a charge-altering Asp-to-His mutant (D46H) expands native cholesterylation activity and retains active-site conformation. Native activity toward cholesterol was established for D46H in vitro using a continuous FRET-based autoprocessing assay and in cellulo with stable expression in human 293T cells. The catalytic efficiency of cholesterylation with D46H is similar to that with wild type (WT), with k max / K M = 2.1 × 10 3 and 3.7 × 10 3 M -1 s -1 , respectively, and an identical p K a = 5.8 is obtained for both residues by NMR. To our knowledge this is the first example where a general base substitution of an Asp for His preserves both the structure and activity as a general base. Surprisingly, D46H exhibits increased catalytic efficiency toward non-native substrates, especially coprostanol (>200-fold) and epicoprostanol (>300-fold). Expanded substrate tolerance is likely due to stabilization by H46 of the negatively charged tetrahedral intermediate using electrostatic interactions, which are less constrained by geometry than H-bond stabilization by D46. In addition to providing fundamental insights into Hh autoprocessing, our findings have important implications for protein engineering and enzyme design.


    Organizational Affiliation

    Department of Chemistry , Binghamton University, State University of New York , Binghamton , New York 13902 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein hedgehog A146Drosophila melanogasterMutation(s): 1 
Gene Names: hhCG4637
Find proteins for Q02936 (Drosophila melanogaster)
Explore Q02936 
Go to UniProtKB:  Q02936
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.381α = 90
b = 78.381β = 90
c = 37.351γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI140726
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI141178
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA206592

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence, Database references